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  <div class="section" id="atomman-atomistic-manipulation-toolkit">
<h1>atomman: Atomistic Manipulation Toolkit<a class="headerlink" href="#atomman-atomistic-manipulation-toolkit" title="Permalink to this headline">¶</a></h1>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>AtomMan: the Atomistic Manipulation Toolkit is a Python library for
creating, representing, manipulating, and analyzing large-scale atomic
systems of atoms. The focus of the package is to facilitate the rapid design
and development of simulations that are fully documented and easily adaptable
to new potentials, configurations, etc.  The code has no requirements that
limit which systems it can be used on, i.e. it should work on Linux, Mac and
Windows computers.</p>
<p>Features:</p>
<ol class="arabic simple">
<li><p>Allows for efficient and fast calculations on millions of atoms, each with
many freely defined per-atom properties.</p></li>
<li><p>Built-in tools for generating and analyzing crystalline defects, such as
point defects, stacking faults, and dislocations.</p></li>
</ol>
<ol class="arabic simple" start="4">
<li><p>Call LAMMPS directly from Python and instantly retrieve the resulting data
or LAMMPS error statement.</p></li>
<li><p>Easily convert systems to/from the other Python atomic representations, such
as ase.Atoms and pymatgen.Structure.</p></li>
<li><p>Can read and dump crystal structure information from a number of formats,
such as LAMMPS data and dump files, and POSCAR.</p></li>
<li><p>Built-in unit conversions.</p></li>
</ol>
</div>
<div class="section" id="installation">
<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h2>
<p>The atomman package is Python 3.7+ compatible.</p>
<p>The latest release can be installed using pip:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">atomman</span>
</pre></div>
</div>
<p>or, alternatively using conda and conda-forge:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">install</span> <span class="n">atomman</span> <span class="o">-</span><span class="n">c</span> <span class="n">conda</span><span class="o">-</span><span class="n">forge</span>
</pre></div>
</div>
<p>For Windows users, it is recommended to use an Anaconda distribution and use
conda to install numpy, scipy, matplotlib, pandas and cython prior to
installing atomman.</p>
<p>Alternatively, all code and documentation can be downloaded from GitHub.</p>
<ul class="simple">
<li><p>The stable releases are available at
<a class="reference external" href="https://github.com/usnistgov/atomman">https://github.com/usnistgov/atomman</a>.</p></li>
<li><p>The working development versions are at
<a class="reference external" href="https://github.com/lmhale99/atomman">https://github.com/lmhale99/atomman</a>.</p></li>
</ul>
</div>
<div class="section" id="tutorials">
<h2>Tutorials<a class="headerlink" href="#tutorials" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="tutorial/index.html">Tutorials</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial/0._Unit_conversions.html">0. Unit conversions</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1._Defining_atomic_systems.html">1. Defining atomic systems</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.1._Box_class.html">1.1. Box class</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.2._Atoms_class.html">1.2. Atoms class</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.3._System_class.html">1.3. System class</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4._Load_and_dump_conversions.html">1.4. Load and dump conversions</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.1._system_model_conversions.html">1.4.1. system_model conversions</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.2._POSCAR_conversions.html">1.4.2. POSCAR conversions</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.3._CIF_conversions.html">1.4.3. CIF conversions</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.4._table_conversions.html">1.4.4. table conversions</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.5._LAMMPS_data_file_conversions.html">1.4.5. LAMMPS data file conversions</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.6._LAMMPS_dump_file_conversions.html">1.4.6. LAMMPS dump file conversions</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.7._ase_and_phonopy_conversions.html">1.4.7. ase and phonopy conversions</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.8._pymatgen_conversions.html">1.4.8. pymatgen conversions</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.9._spglib_conversions.html">1.4.9. spglib conversions</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.10._prototype_loading.html">1.4.10. prototype loading</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.11._crystal_loading.html">1.4.11. crystal loading</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.4.12._DFT_reference_crystal_loading.html">1.4.12. DFT reference crystal loading</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/1.5._Settings_and_databases.html">1.5. Settings and databases</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/2._LAMMPS_functionality.html">2. LAMMPS functionality</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/2.1._Potential_class.html">2.1. Potential class</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/2.2._Running_LAMMPS_and_the_Log_class.html">2.2. Running LAMMPS and the Log class</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/3._Basic_support_and_analysis_tools.html">3. Basic support and analysis tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/3.1._ElasticConstants_class.html">3.1. ElasticConstants class</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/3.2._NeighborList_class.html">3.2. NeighborList class</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/3.3._Region_selectors.html">3.3. Region selectors</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/3.4._Minimum_energy_paths.html">3.4. Minimum energy paths</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/3.5._Cluster_generators.html">3.5. Cluster generators</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/4._Defect_creation_and_analysis.html">4. Defect creation and analysis</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/4.1._Point_defect_generation.html">4.1. Point defect generation</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/4.2._Free_surface_generator.html">4.2. Free surface generator</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/4.3._Stacking_fault_generator.html">4.3. Stacking fault generator</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/4.4._Dislocation_solution_and_generator.html">4.4. Dislocation solution and generator</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/4.5._Gamma_surface_plotting.html">4.5. Gamma surface plotting</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/4.6._Dislocation_analysis_tools.html">4.6. Dislocation analysis tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/4.7._Semidiscrete_variational_Peierls-Nabarro_model.html">4.7. Semidiscrete variational Peierls-Nabarro model</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial/4.8._Strain_class.html">4.8. Strain class</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="section" id="code-documentation">
<h2>Code Documentation<a class="headerlink" href="#code-documentation" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="atomman.html">atomman package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="atomman.html#submodules">Submodules</a><ul>
<li class="toctree-l3"><a class="reference internal" href="atomman.unitconvert.html">unitconvert</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.tools.html">tools</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.region.html">region</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.cluster.html">cluster</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.mep.html">mep</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.lammps.html">lammps</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.library.html">library</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.defect.html">defect</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.plot.html">plot</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="atomman.html#classes">Classes</a><ul>
<li class="toctree-l3"><a class="reference internal" href="atomman.Atoms.html">Atoms</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.Box.html">Box</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.System.html">System</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.ElasticConstants.html">ElasticConstants</a></li>
<li class="toctree-l3"><a class="reference internal" href="atomman.NeighborList.html">NeighborList</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="atomman.html#module-atomman">Functions and attributes</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="section" id="indices-and-tables">
<h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
</ul>
</div>
</div>


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  <h3><a href="#">Table of Contents</a></h3>
  <ul>
<li><a class="reference internal" href="#">atomman: Atomistic Manipulation Toolkit</a><ul>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#installation">Installation</a></li>
<li><a class="reference internal" href="#tutorials">Tutorials</a></li>
<li><a class="reference internal" href="#code-documentation">Code Documentation</a></li>
<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
</ul>
</li>
</ul>

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